[Çözüldü] VCF dosyasına müdahale etme

[shigej38]

Merhabalar arkadaşlar:
Elimde biyoinformatik çalışmalarında kullanılan bir vcf (variant caller format) dosyası var bu dosyanın birinci sütününde yer alan bilgileri değiştirmem gerekiyor. örneğin insan kromozomlarının isimleri olarak NC_000001.10, NC_000002.8, NC_000003.9, ...... , NC_000022.10 şeklinde gidiyor ben bu kromozom isimlerini chr1, chr2, chr3, .... , chr22 şeklinde değiştirmek istiyorum bunu nasıl yapabilirim?
VCF dosyası 4,954,779 adet line içeriyor bunu libre office ile açamıyorum visual code studio ile açtığımda ile takılıp kalıyor bilgisayarım.

ayrıca bu bahsettiğim kromozomların isimleri sadece birinci sütünda bulunmuyor 3 ve 4. sütünlarda bu bilgileri içeriyor onları değiştirmeden sadece birinci sütünü değiştirmem gerekiyor.

Şimdiden Teşekkür Ederim.

Kod Seç Genişlet

sed -i -- 's/eski/yeni/gi' /nerede/bu/dosya

komutu işime yaramıyor çünkü bütün sütünlarda ki bilgileri değiştiriyor.

[Empat]

Bunun için regExp yazmalısınız. Örneğin; Düzenli ifadelerle NC ile başlayan ve x, xx, xxx haneli sayı bitenleri yakalayabilirsiniz.

[shigej38]

[mention=647872]@Empat[/mention]

Biraz daha açabilir misiniz? regExp'i ilk defa duyuyorum

[Amenofis]

Dosyayı sıkıştırıp bir yere atabilirsen indirip bakalım. Belki senin yerine hallederiz.

[Empat]

[mention=647875]@Amenofis[/mention]
Merhaba. İletinizi, daha önceki iletinize dönüştürdüm. Sadece tek bir karakter barındıran anlamsız ve herhangi bir şey ifade etmeyen iletiler, spam olarak değerlendiriliyor ve forum düzenini olumsuz yönde etkiliyor.

.

[mention=647874]@shigej38[/mention]
Bu makaleyi okuyarak hakkında bilgi edinebilirsiniz.

[shigej38]

Sevgili: [mention=647875]@Amenofis[/mention]
düzenlemek istediğim dosyası bu linkten indirebilirsiniz lakin benim yerime yapmanız için değilde dosyayı inceleyebilmeniz için paylaşıyorum zira benim yerime yaparsanız ben * bir şey öğrenmiş olmam sadece şu anlık işim halledilmiş olur. İlginiz için teşekkür ederim.

Dosya

Sevgili: [mention=647886]@Empat[/mention]
bahsettiğiniz makaleyi bugün içerisinde inceleyeceğim teşekkür ederim.

[Amenofis]

Ben sadece dosyayı modifiye etmek için yardım istediğini zannettim. Bunun nasıl yapılacağını öğrenmek istiyorsan en iyisi kendin yapman. Ben python bilmem ama algoritma konusunda yardımcı olabilirim. Sen dosyayı aç, satır satır okumaya başla. NC_0000xx... zaten en başta. xx, "chr" den sonra gelecek numarayı veriyor. chr + xx stringini ilk sütun ile değiştireceksin. Takıldığın yeri sor.


Mesaj tekrarı yüzünden mesajınız birleştirildi. Bu mesajın gönderim tarihi : 18 Temmuz 2019 - 12:54:37
[mention=647886]@Empat[/mention]
Arkadaşım o noktayı koyduysam herhalde mesajımı silmek için koymuşumdur. Eski haline getirmek yerine silmen lazımdı. Dosyayı hemen atmış olsaydı uğraşabilirdim ama artık zor. O yüzden sildim.

[Empat]

[mention=647888]@Amenofis[/mention]
Üyelerin konu veya iletilerini silmiyoruz. Silinmesi gereken konuları bile üyelerin erişimi olmadığı çöp kutusuna taşıyoruz.
Eğer silinmesini istediğiniz bir iletiniz olursa, iletiyi anlam karmaşası yaşatabilecek bir hale döndürmektense, "bu iletimi silebilirsiniz" vb. bir cümle yazabilirsiniz.
Bu sayede, konulardaki kalite ve ciddiyet artmış olur. 

Lütfen kısa süre içerisinde üst üste ileti (flood) atmayýn.

Bunun yerine daha önce attığınız iletiyi düzenleyin.

[mhmtkrktr]

benim yerime yaparsanız ben * bir şey öğrenmiş olmam

Tek satır komutu, yapmadan tarif etmenin bir yolunu bulamadım 
Bu konuda hala iddialıysan, bundan sonra ki satırlara bakma 

Kod Seç Genişlet

NcConvert() { awk '/^#/' "$1" > "$2" ; awk '!/^#/' "$1"|awk '{sub(/^NC_[0-9]*.[0-9]*/, "chr_"FNR); print;next;}{print}' >>"$2";}; NcConvert "Kaynak_dosya.vcf" "Hedef_dosya_adı.vcf"

Örnek:

Kod Seç Genişlet

##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=NC_000001.10,length=249250621,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr1.fna.gz>
##contig=<ID=NC_000002.11,length=243199373,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr2.fna.gz>
##contig=<ID=NC_000003.11,length=198022430,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr3.fna.gz>
##contig=<ID=NC_000004.11,length=191154276,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr4.fna.gz>
##contig=<ID=NC_000005.9,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr5.fna.gz,length=180915260>
##contig=<ID=NC_000006.11,length=171115067,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr6.fna.gz>
##contig=<ID=NC_000007.13,length=159138663,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr7.fna.gz>
##contig=<ID=NC_000008.10,length=146364022,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr8.fna.gz>
##contig=<ID=NC_000009.11,length=141213431,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr9.fna.gz>
##contig=<ID=NC_000010.10,length=135534747,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr10.fna.gz>
##contig=<ID=NC_000011.9,length=135006516,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr11.fna.gz>
##contig=<ID=NC_000012.11,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr12.fna.gz,length=133851895>
##contig=<ID=NC_000013.10,length=115169878,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr13.fna.gz>
##contig=<ID=NC_000014.8,length=107349540,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr14.fna.gz>
##contig=<ID=NC_000015.9,length=102531392,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr15.fna.gz>
##contig=<ID=NC_000016.9,length=90354753,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr16.fna.gz>
##contig=<ID=NC_000017.10,length=81195210,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr17.fna.gz>
##contig=<ID=NC_000018.9,length=78077248,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr18.fna.gz>
##contig=<ID=NC_000019.9,length=59128983,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr19.fna.gz>
##contig=<ID=NC_000020.10,length=63025520,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr20.fna.gz>
##contig=<ID=NC_000021.8,length=48129895,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr21.fna.gz>
##contig=<ID=NC_000022.10,length=51304566,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr22.fna.gz>
##contig=<ID=NC_000023.10,length=155270560,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chrX.fna.gz>
##contig=<ID=NC_000024.9,length=59373566,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chrY.fna.gz>
##INFO=<ID=GENE,Number=.,Type=String,Description="Genes for this variant">
##INFO=<ID=HGVSG,Number=1,Type=String,Description="HGVS genomic notation for this variant">
##INFO=<ID=MMCNT1,Number=1,Type=Integer,Description="Count of Mastermind articles with cDNA matches for this specific variant">
##INFO=<ID=MMCNT2,Number=1,Type=Integer,Description="Count of Mastermind articles with variants either explicitly matching at the cDNA level or given only at protein level">
##INFO=<ID=MMCNT3,Number=1,Type=Integer,Description="Count of Mastermind articles including other DNA-level variants resulting in the same amino acid change">
##INFO=<ID=MMID3,Number=.,Type=String,Description="Mastermind variant identifiers, as gene:key, for MMCNT3">
##INFO=<ID=MMURI3,Number=.,Type=String,Description="Mastermind search URI for articles including other DNA-level variants resulting in the same amino acid change">
##createdDate=Fri, 14 Jun 2019 00:35:11 UTC
##fileTimestamp=2019-06-14T00:35:11Z
##reference=GRCh37.p13
##bcftools_normVersion=1.9+htslib-1.9
##bcftools_normCommand=norm -f /data/GCF_000001405.25_GRCh37.p13_genomic.fna.gz -c w -o /cvr/cvr_20190613.norm.vcf.gz -O z --threads 4 /cvr/cvr_20190613.raw.vcf.gz; Date=Fri Jun 14 00:35:40 2019
#CHROM POS ID REF ALT QUAL FILTER INFO
chr_1 86921073 . GAT AAC . PASS HGVSG=NC_000001.10:g.86921073_86921075delinsAAC;GENE=CLCA2;MMCNT1=0;MMCNT2=0;MMCNT3=1;MMID3=CLCA2:D899N;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA2&mutation=CLCA2:D899N&ref=cvr
chr_2 86921190 . AAT CAA . PASS HGVSG=NC_000001.10:g.86921190_86921192delinsCAA;GENE=CLCA2;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA2:N938Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA2&mutation=CLCA2:N938Q&ref=cvr
chr_3 86921190 . AAT CAG . PASS HGVSG=NC_000001.10:g.86921190_86921192delinsCAG;GENE=CLCA2;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA2:N938Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA2&mutation=CLCA2:N938Q&ref=cvr
chr_4 86934661 . CC TA . PASS HGVSG=NC_000001.10:g.86934661_86934662delinsTA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:P3X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:P3X&ref=cvr
chr_5 86934661 . CC TG . PASS HGVSG=NC_000001.10:g.86934661_86934662delinsTG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:P3X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:P3X&ref=cvr
chr_6 86934661 . CCA TAG . PASS HGVSG=NC_000001.10:g.86934661_86934663delinsTAG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:P3X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:P3X&ref=cvr
chr_7 86934679 . T C . PASS HGVSG=NC_000001.10:g.86934679T>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_8 86934679 . TTC CTA . PASS HGVSG=NC_000001.10:g.86934679_86934681delinsCTA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_9 86934679 . TTC CTG . PASS HGVSG=NC_000001.10:g.86934679_86934681delinsCTG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_10 86934679 . TTC CTT . PASS HGVSG=NC_000001.10:g.86934679_86934681delinsCTT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_11 86934681 . C A . PASS HGVSG=NC_000001.10:g.86934681C>A;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_12 86934681 . C G . PASS HGVSG=NC_000001.10:g.86934681C>G;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:F9L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:F9L&ref=cvr
chr_13 86934689 . T G . PASS HGVSG=NC_000001.10:g.86934689T>G;GENE=CLCA1;MMCNT1=2;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:I12S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:I12S&ref=cvr
chr_14 86934717 . T C . PASS HGVSG=NC_000001.10:g.86934717T>C;GENE=CLCA1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S21S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S21S&ref=cvr
chr_15 86934734 . T A . PASS HGVSG=NC_000001.10:g.86934734T>A;GENE=CLCA1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:L27Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L27Q&ref=cvr
chr_16 86934761 . T C . PASS HGVSG=NC_000001.10:g.86934761T>C;GENE=CLCA1;MMCNT1=2;MMCNT2=3;MMCNT3=3;MMID3=CLCA1:V36A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:V36A&ref=cvr
chr_17 86934761 . TC CA . PASS HGVSG=NC_000001.10:g.86934761_86934762delinsCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=3;MMID3=CLCA1:V36A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:V36A&ref=cvr
chr_18 86934761 . TC CG . PASS HGVSG=NC_000001.10:g.86934761_86934762delinsCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=3;MMID3=CLCA1:V36A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:V36A&ref=cvr
chr_19 86934761 . TC CT . PASS HGVSG=NC_000001.10:g.86934761_86934762delinsCT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=3;MMID3=CLCA1:V36A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:V36A&ref=cvr
chr_20 86939223 . C A . PASS HGVSG=NC_000001.10:g.86939223C>A;GENE=CLCA1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:L96I;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L96I&ref=cvr
chr_21 86939423 . G T . PASS HGVSG=NC_000001.10:g.86939423G>T;GENE=CLCA1;MMCNT1=2;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:L105L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L105L&ref=cvr
chr_22 86939433 . T G . PASS HGVSG=NC_000001.10:g.86939433T>G;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S109A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S109A&ref=cvr
chr_23 86939433 . TCT GCA . PASS HGVSG=NC_000001.10:g.86939433_86939435delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S109A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S109A&ref=cvr
chr_24 86939433 . TCT GCC . PASS HGVSG=NC_000001.10:g.86939433_86939435delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S109A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S109A&ref=cvr
chr_25 86939433 . TCT GCG . PASS HGVSG=NC_000001.10:g.86939433_86939435delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S109A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S109A&ref=cvr
chr_26 86939499 . AGG CAC . PASS HGVSG=NC_000001.10:g.86939499_86939501delinsCAC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:R131H;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R131H&ref=cvr
chr_27 86939499 . AGG CAT . PASS HGVSG=NC_000001.10:g.86939499_86939501delinsCAT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:R131H;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R131H&ref=cvr
chr_28 86939502 . A G . PASS HGVSG=NC_000001.10:g.86939502A>G;GENE=CLCA1;MMCNT1=2;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:I132V;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:I132V&ref=cvr
chr_29 86942145 . CA GC . PASS HGVSG=NC_000001.10:g.86942145_86942146delinsGC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H156A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H156A&ref=cvr
chr_30 86942145 . CAT GCA . PASS HGVSG=NC_000001.10:g.86942145_86942147delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H156A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H156A&ref=cvr
chr_31 86942145 . CAT GCC . PASS HGVSG=NC_000001.10:g.86942145_86942147delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H156A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H156A&ref=cvr
chr_32 86942145 . CAT GCG . PASS HGVSG=NC_000001.10:g.86942145_86942147delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H156A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H156A&ref=cvr
chr_33 86942148 . G C . PASS HGVSG=NC_000001.10:g.86942148G>C;GENE=CLCA1;MMCNT1=0;MMCNT2=4;MMCNT3=4;MMID3=CLCA1:E157Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E157Q&ref=cvr
chr_34 86942148 . GAG CAA . PASS HGVSG=NC_000001.10:g.86942148_86942150delinsCAA;GENE=CLCA1;MMCNT1=0;MMCNT2=4;MMCNT3=4;MMID3=CLCA1:E157Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E157Q&ref=cvr
chr_35 86942157 . CA GC . PASS HGVSG=NC_000001.10:g.86942157_86942158delinsGC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H160A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H160A&ref=cvr
chr_36 86942157 . CAT GCA . PASS HGVSG=NC_000001.10:g.86942157_86942159delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H160A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H160A&ref=cvr
chr_37 86942157 . CAT GCC . PASS HGVSG=NC_000001.10:g.86942157_86942159delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H160A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H160A&ref=cvr
chr_38 86942157 . CAT GCG . PASS HGVSG=NC_000001.10:g.86942157_86942159delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:H160A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:H160A&ref=cvr
chr_39 86942179 . A C . PASS HGVSG=NC_000001.10:g.86942179A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D167A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D167A&ref=cvr
chr_40 86942179 . AC CA . PASS HGVSG=NC_000001.10:g.86942179_86942180delinsCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D167A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D167A&ref=cvr
chr_41 86942179 . AC CG . PASS HGVSG=NC_000001.10:g.86942179_86942180delinsCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D167A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D167A&ref=cvr
chr_42 86942179 . AC CT . PASS HGVSG=NC_000001.10:g.86942179_86942180delinsCT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D167A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D167A&ref=cvr
chr_43 86942182 . A C . PASS HGVSG=NC_000001.10:g.86942182A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E168A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E168A&ref=cvr
chr_44 86942182 . AG CA . PASS HGVSG=NC_000001.10:g.86942182_86942183delinsCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E168A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E168A&ref=cvr
chr_45 86942182 . AG CC . PASS HGVSG=NC_000001.10:g.86942182_86942183delinsCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E168A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E168A&ref=cvr
chr_46 86942182 . AG CT . PASS HGVSG=NC_000001.10:g.86942182_86942183inv;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E168A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E168A&ref=cvr
chr_47 86942208 . TT AC . PASS HGVSG=NC_000001.10:g.86942208_86942209delinsAC;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:L177T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L177T&ref=cvr
chr_48 86942208 . TTA ACC . PASS HGVSG=NC_000001.10:g.86942208_86942210delinsACC;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:L177T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L177T&ref=cvr
chr_49 86942208 . TTA ACG . PASS HGVSG=NC_000001.10:g.86942208_86942210delinsACG;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:L177T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L177T&ref=cvr
chr_50 86942208 . TTA ACT . PASS HGVSG=NC_000001.10:g.86942208_86942210delinsACT;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:L177T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:L177T&ref=cvr
chr_51 86947973 . G T . PASS HGVSG=NC_000001.10:g.86947973G>T;GENE=CLCA1;MMCNT1=2;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:V215L;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:V215L&ref=cvr
chr_52 86947977 . C T . PASS HGVSG=NC_000001.10:g.86947977C>T;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216I;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216I&ref=cvr
chr_53 86947977 . CA TC . PASS HGVSG=NC_000001.10:g.86947977_86947978delinsTC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216I;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216I&ref=cvr
chr_54 86947977 . CA TT . PASS HGVSG=NC_000001.10:g.86947977_86947978delinsTT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216I;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216I&ref=cvr
chr_55 86947978 . A C . PASS HGVSG=NC_000001.10:g.86947978A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216T&ref=cvr
chr_56 86947978 . A G . PASS HGVSG=NC_000001.10:g.86947978A>G;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216T&ref=cvr
chr_57 86947978 . A T . PASS HGVSG=NC_000001.10:g.86947978A>T;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:T216T;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T216T&ref=cvr
chr_58 86947995 . G A . PASS HGVSG=NC_000001.10:g.86947995G>A;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:G222E;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:G222E&ref=cvr
chr_59 86947995 . GA AG . PASS HGVSG=NC_000001.10:g.86947995_86947996delinsAG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:G222E;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:G222E&ref=cvr
chr_60 86948036 . T G . PASS HGVSG=NC_000001.10:g.86948036T>G;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S236A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S236A&ref=cvr
chr_61 86948036 . TCT GCA . PASS HGVSG=NC_000001.10:g.86948036_86948038delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S236A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S236A&ref=cvr
chr_62 86948036 . TCT GCC . PASS HGVSG=NC_000001.10:g.86948036_86948038delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S236A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S236A&ref=cvr
chr_63 86948036 . TCT GCG . PASS HGVSG=NC_000001.10:g.86948036_86948038delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S236A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S236A&ref=cvr
chr_64 86948066 . GTAAGTACCTTGTTCTCACCCCCTCCCCCAGATTCTTATGAATTTAGTGAGGCTTTTACTCCAAGTGCTCCAAGGGAGAATCAAAGTTTAGAGAAATCATCAGTGAGCAGTGGATTATCTCTGGGACAAGCTGGGTGTGCAAGTCAAGGATAAAGTCCTGTCTTCCTTCCCCTTACCCTCCTCGTGTCCACGCTTTCTTCTCCATCATCTCCCTCCCACTAGTTTTTAGTTCAAGTGCTTAGGATTACTTTAAATACTCACAAAGGCATACAAGCACACACATTCTTACTTAAATAAGGACTTAACCCAGGGGGATTAGGCAGTTCCTTTTATTAGTTAATAAAGACATGATCAGTAGGCTCTTGATTTAACTTTCAGAGAGCTCTTTTCAGACTGCATGTTTGCTTTTGGTTGTTAACTGAAATTTTCTATCTTTTTAAGAGTGTTGGTTACATTAGGGAGTTTACACATAGTTTAAATAGCTTTAAATAGTTTTAAAATTCTTAATTTTTTTAATGAATAACTGGTCATAAAATGAACTTGGCCAGTTATTGATATTACTGCTAAATATATAAATCAGAAATTTTGCGCAAAATGAGATTGAAGGCATCAGTTAACTGACTTCAGTGGGAAGTCTCTCTTGTCTTCCAGTCTCATATAAAATTACATTTTCCTTTTGGAATAGAGGGTGCAATAAATTGCAAGAGTCTGTTCAACAGGAATGGAGCATAAGTTTTTAAAATGTGATGCACCATGGCTCACCAGGCCCATCGTCCTTCAATTTGGCATTGCAGTCCATTCCCAGGCCTATTCAGAAACTTCCAGGAGGAGGCCCAGATTATATATTTTAAATTAGCCACAGAGTTAAATATGATGCCTAGTCAGGTGTGGAAGCCTCTGCCTGGGGTTTACACAAACGTTTTTCAGGTCTGCTTCCTAAAAAGTATCCATATTGATAACATAAAAACATTACCGAAACACATGACCTGAAAAACGCACATAAAGAGAAAAATGTTGTACAACTAATGATTACTTTCTAAATTAATAGCATCCCAGATATTAGGATTTGTAATTGCATGATAATATTGTAAAGTCACTGAGAGGAGGAATCATGTTACTTTTCTTTTGTATACTATGCCTTAAAAAAAAAATCCCCCACAGGCGAGAGATATAAATACTAGCAAGTGTTATATGACATAAGAAAGGTAAAGGAACCATCATTTATTGGCTGTGTTAGTATTGACCTTAGTGCATATATTCTCATTTATTTCCTGCATAATAACTATCACTATTTTGTAGATTTAATAATTCAGGTGCAGAGAGGTTAAGGTTACTCAAAAAATAACAAAGTCATATTGAGTTTTTGTTATGTGTCAGGCACTAGGGCTAAATTTTGAGGAAGCAAAATTTAGTAAGCAGGTTTCTGTAATAGATGGTGTATTAATTCATTTTCACACCTCTATAAACTATATCTAAGACTGGATAATTTATAAATGAAAGAGGTTTCATTGACTCACAGTTCCACATGGCTAGGGAGGCCTCAGGAAACTTACCATCATGGTGGAAGGCGAAGGAGAAGCAAGGCACACCTTACGAGGTGGCAGGAGAGAGAGAATGCAAGGGAAATTGCCGCTTACAAAATCATCAGATTACGTGGGAACTCACTCAATATCACAAGAACAGCATGGAGGAAACCATCTCGATGATCCAATCACCTCCCACCAGATCCCTCCCTCGACACGTGGGGATTACAAATCAAGATGAGATTTGGGTGGGACACAGAGCCAAACCATATCAGATGGATTTACAGTCCAGTAAGTGCACTGCAATGTTAAAGGGGCCTTATTGAAATTTCTACAAGATATCGTGAAGCTATAAAGGGTGGAATGGAAATTCTCAGGAGGAAGAGTAGAAAATGGAGAAACATTTCGGAAGTGACTTTTTGGCTGAACATGAAGGTAGAGTTTACAACGTAGAAGACAGAGGAGGAGCAATAGAGATGCCAAAGGCTGGCAAGTTTGGGAACTGACAGGCTATAGTGGGGTAAATTAGAGACATGGAATACACAGCCAGAATGAGAATGGAGAATGAAGCAAAGCTCCAAGTCATAGAGTTTGCCATTGGTATATGAAGAGTGGATTGTAATGTATGAACAATTAAAGCAGAGGAGTAAGAGGAAAGACTCTCAGGCAGCTGTGAGGTGGAACAAACAGAGAGGAAACAAGATGGAAAAGTCACAAAGTAAACTGCAATCGTCTGAGGGAGGGACTGTGATGGCTTGGGTGATGGATATTTCATTGGAGATGGAGAAAAGATGAAGAAATTGAGATATAGTGAAGTGCACTGGTCTTGGGTACTTTTTAGGAGGGAAAAGGTAGGAAAACTTCCAGTTTCCTAATTTTGGTGATGGGGTGCATAGTGGTGACATCAAGTTAGGAAATACCTGAGGAGGAGGAGCAGATGGGAGAAAAGTGATAAGGTCAATAATGAACATGTGGAGTTTGAGGCGCATGTGAGACATCCAAGTGGATTTTGGAGAGAGCTGGAACATTGGGAGTTGAAGGTTAGAATATAGTGTGTTGGTAAATGAGTGAGAAGTAAGGAAGTGGAGTTTGGTGGTATAAGGGTGGAGAGATAAGATGGTTCCAAGAGAGGAATGCTGGAGAGGGTGCTATGGAGAGAGCAGTGATGGCTTGAAATGGTAAATTTGAGGAGTAGGAAGGAAACCAAAAAGAGGAGGTAAATGGATTGCTGAGGAGCACTAAGGGTCCAATGAGATTGAAGGCCTGGTTTAAGGTAGGAAATCTGCATTATTACTGTGATTTTCCCCAGCACTGTTCCACAGTGATTGTGCAATTGAGCCAAGGTTATGCATTAGCAGAGCAGACAGGTCTAACAAATTATTAAATATTCTACCACATAGTTTACCATTATCTATATAATTTCATTGACAATTTCA ACT . PASS HGVSG=NC_000001.10:g.86948066_86951024delinsACT;GENE=CLCA1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S245ins;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S245ins&ref=cvr
chr_65 86951059 . AA GC . PASS HGVSG=NC_000001.10:g.86951059_86951060delinsGC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:K257A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:K257A&ref=cvr
chr_66 86951059 . AAA GCC . PASS HGVSG=NC_000001.10:g.86951059_86951061delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:K257A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:K257A&ref=cvr
chr_67 86951059 . AAA GCG . PASS HGVSG=NC_000001.10:g.86951059_86951061delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:K257A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:K257A&ref=cvr
chr_68 86951059 . AAA GCT . PASS HGVSG=NC_000001.10:g.86951059_86951061delinsGCT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:K257A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:K257A&ref=cvr
chr_69 86951098 . C G . PASS HGVSG=NC_000001.10:g.86951098C>G;GENE=CLCA1;MMCNT1=2;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:R270G;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R270G&ref=cvr
chr_70 86951098 . C T . PASS HGVSG=NC_000001.10:g.86951098C>T;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:R270X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R270X&ref=cvr
chr_71 86951098 . CG TA . PASS HGVSG=NC_000001.10:g.86951098_86951099delinsTA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:R270X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R270X&ref=cvr
chr_72 86951098 . CGA TAG . PASS HGVSG=NC_000001.10:g.86951098_86951100delinsTAG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:R270X;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:R270X&ref=cvr
chr_73 86951206 . ATT TGG . PASS HGVSG=NC_000001.10:g.86951206_86951208delinsTGG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:I306W;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:I306W&ref=cvr
chr_74 86951224 . G A . PASS HGVSG=NC_000001.10:g.86951224G>A;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312N;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312N&ref=cvr
chr_75 86951224 . GAC AAT . PASS HGVSG=NC_000001.10:g.86951224_86951226delinsAAT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312N;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312N&ref=cvr
chr_76 86951225 . A C . PASS HGVSG=NC_000001.10:g.86951225A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312A&ref=cvr
chr_77 86951225 . AC CA . PASS HGVSG=NC_000001.10:g.86951225_86951226delinsCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312A&ref=cvr
chr_78 86951225 . AC CG . PASS HGVSG=NC_000001.10:g.86951225_86951226delinsCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312A&ref=cvr
chr_79 86951225 . AC CT . PASS HGVSG=NC_000001.10:g.86951225_86951226delinsCT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D312A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D312A&ref=cvr
chr_80 86951230 . T G . PASS HGVSG=NC_000001.10:g.86951230T>G;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S314A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S314A&ref=cvr
chr_81 86951230 . TCT GCA . PASS HGVSG=NC_000001.10:g.86951230_86951232delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S314A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S314A&ref=cvr
chr_82 86951230 . TCT GCC . PASS HGVSG=NC_000001.10:g.86951230_86951232delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S314A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S314A&ref=cvr
chr_83 86951230 . TCT GCG . PASS HGVSG=NC_000001.10:g.86951230_86951232delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S314A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S314A&ref=cvr
chr_84 86951236 . AG GC . PASS HGVSG=NC_000001.10:g.86951236_86951237delinsGC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S316A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S316A&ref=cvr
chr_85 86951236 . AGC GCA . PASS HGVSG=NC_000001.10:g.86951236_86951238delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S316A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S316A&ref=cvr
chr_86 86951236 . AGC GCG . PASS HGVSG=NC_000001.10:g.86951236_86951238delinsGCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S316A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S316A&ref=cvr
chr_87 86951236 . AGC GCT . PASS HGVSG=NC_000001.10:g.86951236_86951238inv;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:S316A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:S316A&ref=cvr
chr_88 86952323 . AA TC . PASS HGVSG=NC_000001.10:g.86952323_86952324delinsTC;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_89 86952323 . AAT TCA . PASS HGVSG=NC_000001.10:g.86952323_86952325delinsTCA;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_90 86952323 . AAT TCC . PASS HGVSG=NC_000001.10:g.86952323_86952325delinsTCC;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_91 86952323 . AAT TCG . PASS HGVSG=NC_000001.10:g.86952323_86952325delinsTCG;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_92 86952324 . A G . PASS HGVSG=NC_000001.10:g.86952324A>G;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_93 86952324 . AT GC . PASS HGVSG=NC_000001.10:g.86952324_86952325delinsGC;GENE=CLCA1;MMCNT1=0;MMCNT2=0;MMCNT3=3;MMID3=CLCA1:N357S;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:N357S&ref=cvr
chr_94 86952401 . A G . PASS HGVSG=NC_000001.10:g.86952401A>G;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:T383A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T383A&ref=cvr
chr_95 86952401 . ACG GCA . PASS HGVSG=NC_000001.10:g.86952401_86952403delinsGCA;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:T383A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T383A&ref=cvr
chr_96 86952401 . ACG GCC . PASS HGVSG=NC_000001.10:g.86952401_86952403delinsGCC;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:T383A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T383A&ref=cvr
chr_97 86952401 . ACG GCT . PASS HGVSG=NC_000001.10:g.86952401_86952403delinsGCT;GENE=CLCA1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CLCA1:T383A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:T383A&ref=cvr
chr_98 86954731 . A C . PASS HGVSG=NC_000001.10:g.86954731A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D412A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D412A&ref=cvr
chr_99 86954731 . AT CA . PASS HGVSG=NC_000001.10:g.86954731_86954732delinsCA;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D412A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D412A&ref=cvr
chr_100 86954731 . AT CC . PASS HGVSG=NC_000001.10:g.86954731_86954732delinsCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D412A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D412A&ref=cvr
chr_101 86954731 . AT CG . PASS HGVSG=NC_000001.10:g.86954731_86954732delinsCG;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:D412A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:D412A&ref=cvr
chr_102 86954785 . C A . PASS HGVSG=NC_000001.10:g.86954785C>A;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:A430D;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:A430D&ref=cvr
chr_103 86954785 . CC AT . PASS HGVSG=NC_000001.10:g.86954785_86954786delinsAT;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:A430D;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:A430D&ref=cvr
chr_104 86954827 . A C . PASS HGVSG=NC_000001.10:g.86954827A>C;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E444A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E444A&ref=cvr
chr_105 86954827 . AA CC . PASS HGVSG=NC_000001.10:g.86954827_86954828delinsCC;GENE=CLCA1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CLCA1:E444A;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CLCA1&mutation=CLCA1:E444A&ref=cvr
chr_106

[shigej38]

Sevgili: [mention=647894]@mhmtkrktr[/mention]


Vermiş olduğunuz dosya içeriğinde chr_106'a kadar uzanmakta ancak dosyanın barındırdığı insan genomu 24 kromozomdan oluşmakta bunlarda 1,2,3,4,5,....20,21,22,X ve Y şeklinde bulunuyorlar. Ancak hatanın dosya içeriğinin ne olduğunu bilmeden komutu ona göre yazdığınız göz önünde bulundurulur ise komutta gerekli düzenlemeler yapılarak istenilen sonuç elde edilebilecektir. Benim amacım hangi yoldan yapmam gerektiğini ögrenmekti ilginiz için teşekkür ederim.

sanırım burda dediğim olay yanlış anlaşılmış

benim yerime yaparsanız ben * bir şey öğrenmiş olmam sadece şu anlık işim halledilmiş olur. İlginiz için teşekkür ederim.

burda benim demek istediğim olay gerekli düzenlemeyi yapıp sana dosyayı gönderelim gibi * bir şey istemediğimi belirtmekti.

[mhmtkrktr]

chr_106 benim metin editöründen örnek olarak kopyaladığım bölüm. Milyonlarca satırın tamamını buraya alıntılamam mümkün değil. Kendi içeriğinde denediğin zaman, tamamının benzer sıralamayla düzenlendiğini görebilirsin.

insan genomu 24 kromozomdan oluşmakta bunlarda 1,2,3,4,5,....20,21,22,X ve Y şeklinde bulunuyorlar.

Bu işler bizim konumuz, kapalı çarşıda esnaflık yaptık, insan sarrafı sayılırız. Adamı alıp 1,2,3 diye sıraya dizmek kolay da, o X ve Y nedir. 
Sonucun içinde buna benzer değerlerde mi olacak, yoksa bilgi olarak mı yazdın?

"Hedef dosyayı" fonksiyonun için rasgele oluşturup, mv ile "kaynak dosya" üzerine de taşıyabilisin. Bu durum da, "kaynak dosya"nın kendisi değişmiş olur. Ben kaynağın nereden geldiğini bilmediğim için "hedef dosya" olarak dışarıda bıraktım.

[shigej38]

Bu işler bizim konumuz, kapalı çarşıda esnaflık yaptık, insan sarrafı sayılırız. Adamı alıp 1,2,3 diye sıraya dizmek kolay da, o X ve Y nedir. 
Sonucun içinde buna benzer değerlerde mi olacak, yoksa bilgi olarak mı yazdın?

insan kromozomlarının isimleri o X ve Y karakterleri dosyanın içerisinde ki 23 ve 24 sayıları X ve Y kromozomlarını temsil etmekte.
verdiğiniz komutun girintilerini tam olarak anlayamadım biraz daha açık olarak yazabilir misiniz? [mention=647920]@mhmtkrktr[/mention]

[mhmtkrktr]

   

Awk bu iş için ideal ve aynı zaman da en hızlı komut. Fakat 'sed -i' gibi doğrudan verilen dosyanın için de değişiklik yapamaz. Bunu yapmak için, 'mv' ile çıkış dosyası, giriş dosyasının üzerine yazılabilir. Aşağı da bu şekilde çalışacak hali var. (Not: kaynak dosyasının kendisi değişecektir)

Kod Seç Genişlet

NcConvert() { F="VCF_${RANDOM}.vcf";awk '/^#/' "$1" > "$F";awk '!/^#/' "$1"|awk '{sub(/^NC_[0-9]*.[0-9]*/, "chr_"FNR); print;next;}{print}' >>"$F" && mv -v "$F" "$1";}; NcConvert 'Kaynak_Dosya.vcf'

Örnek;

Komuttan önce, son 10 satır

Kod Seç Genişlet

cat ~/Masaüstü/mastermind_cited_variants_reference-2019.06.14-grch37.vcf | tail -10

Kod Seç Genişlet

NC_000024.9 27768619 . T TA . PASS HGVSG=NC_000024.9:g.27768620dup;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:I11fs;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:I11fs&ref=cvr
NC_000024.9 27768701 . T C . PASS HGVSG=NC_000024.9:g.27768701T>C;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:W38R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:W38R&ref=cvr
NC_000024.9 27768722 . AT CG . PASS HGVSG=NC_000024.9:g.27768722_27768723delinsCG;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27768722 . ATG CGA . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27768722 . ATG CGC . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGC;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27768722 . ATG CGT . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGT;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27768723 . T G . PASS HGVSG=NC_000024.9:g.27768723T>G;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27768723 . TG GA . PASS HGVSG=NC_000024.9:g.27768723_27768724delinsGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
NC_000024.9 27769209 . T A . PASS HGVSG=NC_000024.9:g.27769209T>A;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr
NC_000024.9 27769209 . TG AA . PASS HGVSG=NC_000024.9:g.27769209_27769210delinsAA;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr

Komuttan sonra, son 10 satır

Kod Seç Genişlet

cat ~/Masaüstü/mastermind_cited_variants_reference-2019.06.14-grch37.vcf | tail -10

Kod Seç Genişlet

chr_4954731 27768619 . T TA . PASS HGVSG=NC_000024.9:g.27768620dup;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:I11fs;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:I11fs&ref=cvr
chr_4954732 27768701 . T C . PASS HGVSG=NC_000024.9:g.27768701T>C;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:W38R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:W38R&ref=cvr
chr_4954733 27768722 . AT CG . PASS HGVSG=NC_000024.9:g.27768722_27768723delinsCG;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954734 27768722 . ATG CGA . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954735 27768722 . ATG CGC . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGC;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954736 27768722 . ATG CGT . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGT;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954737 27768723 . T G . PASS HGVSG=NC_000024.9:g.27768723T>G;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954738 27768723 . TG GA . PASS HGVSG=NC_000024.9:g.27768723_27768724delinsGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954739 27769209 . T A . PASS HGVSG=NC_000024.9:g.27769209T>A;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr
chr_4954740 27769209 . TG AA . PASS HGVSG=NC_000024.9:g.27769209_27769210delinsAA;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr

[shigej38]

Sevgili: [mention=647944]@mhmtkrktr[/mention]

sanırım yanlış anlattım istediğim olayı

Kod Seç Genişlet

NC_000001.10 chr1
NC_000002.10 chr2
.
.
.
.
.
NC_000023.(blabla) chrX
NC_000024.(blabla) chrY

şeklinde değişmesi gerekiyor senin verdiğin komut satır sayısı olarak 'chr' sonuna ekliyor ancak benim yapmak istediğim şey tam olarak bu şekilde değil.

Komuttan sonra, son 10 satır

Kod Seç Genişlet

cat ~/Masaüstü/mastermind_cited_variants_reference-2019.06.14-grch37.vcf | tail -10

Kod Seç Genişlet

chr_4954731 27768619 . T TA . PASS HGVSG=NC_000024.9:g.27768620dup;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:I11fs;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:I11fs&ref=cvr
chr_4954732 27768701 . T C . PASS HGVSG=NC_000024.9:g.27768701T>C;GENE=CDY1;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=CDY1:W38R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:W38R&ref=cvr
chr_4954733 27768722 . AT CG . PASS HGVSG=NC_000024.9:g.27768722_27768723delinsCG;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954734 27768722 . ATG CGA . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954735 27768722 . ATG CGC . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGC;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954736 27768722 . ATG CGT . PASS HGVSG=NC_000024.9:g.27768722_27768724delinsCGT;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954737 27768723 . T G . PASS HGVSG=NC_000024.9:g.27768723T>G;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954738 27768723 . TG GA . PASS HGVSG=NC_000024.9:g.27768723_27768724delinsGA;GENE=CDY1;MMCNT1=0;MMCNT2=2;MMCNT3=2;MMID3=CDY1:M45R;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M45R&ref=cvr
chr_4954739 27769209 . T A . PASS HGVSG=NC_000024.9:g.27769209T>A;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr
chr_4954740 27769209 . TG AA . PASS HGVSG=NC_000024.9:g.27769209_27769210delinsAA;GENE=CDY1;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=CDY1:M207K;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=CDY1&mutation=CDY1:M207K&ref=cvr

Kod Seç Genişlet

sed -i  's/NC_000001.10/chr1/gi' /nerede/bu/dosya

bu komutu kullandığım zaman istediğim sonucu elde ediyorum fakat dosya içerisinde 8. sütüna denk gelen kısımda ki bilgilerde kromozom isimlerini barındırıyor ve sed komutu bunuda değiştiriyor. bunun değişmesini istemiyorum ben sadece 1. sutünde bulunan kromozom isimlerini NC versiyonlarından chr versiyonlarına dönüştürmek istiyorum.


yani son durumda istediğim durum şu şekilde olması gerekiyor:
Eğer header kısmını incelerseniz chr1 chr2 ..... chr22 chrX chrY şeklinde bulunuyor ancak bunu "sed" komutu ile yaptım ve 8. sütünda (INFO sütünü) bulunan NC numaraları da değişti benim istemediğim durum bu 8. sütünda ki NC numaralarının sabit kalıp sadece 1. sütünde bulunan NC numaralarını karşılık gelen chr numaraları şeklinde düzenlemek

Kod Seç Genişlet

head -n 50 Desktop/mastermind_cited_variants_reference-2019.06.14-grch37.vcf
##fileformat=VCFv4.2
##FILTER=<ID=PASS,Description="All filters passed">
##contig=<ID=chr1,length=249250621,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr1.fna.gz>
##contig=<ID=chr2,length=243199373,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr2.fna.gz>
##contig=<ID=chr3,length=198022430,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr3.fna.gz>
##contig=<ID=chr4,length=191154276,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr4.fna.gz>
##contig=<ID=chr5,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr5.fna.gz,length=180915260>
##contig=<ID=chr6,length=171115067,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr6.fna.gz>
##contig=<ID=chr7,length=159138663,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr7.fna.gz>
##contig=<ID=chr8,length=146364022,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr8.fna.gz>
##contig=<ID=chr9,length=141213431,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr9.fna.gz>
##contig=<ID=chr10,length=135534747,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr10.fna.gz>
##contig=<ID=chr11,length=135006516,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr11.fna.gz>
##contig=<ID=chr12,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr12.fna.gz,length=133851895>
##contig=<ID=chr13,length=115169878,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr13.fna.gz>
##contig=<ID=chr14,length=107349540,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr14.fna.gz>
##contig=<ID=chr15,length=102531392,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr15.fna.gz>
##contig=<ID=chr16,length=90354753,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr16.fna.gz>
##contig=<ID=chr17,length=81195210,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr17.fna.gz>
##contig=<ID=chr18,length=78077248,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr18.fna.gz>
##contig=<ID=chr19,length=59128983,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr19.fna.gz>
##contig=<ID=chr20,length=63025520,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr20.fna.gz>
##contig=<ID=chr21,length=48129895,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr21.fna.gz>
##contig=<ID=chr22,length=51304566,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chr22.fna.gz>
##contig=<ID=chrX,length=155270560,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chrX.fna.gz>
##contig=<ID=chrY,length=59373566,URL=ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/vertebrate_mammalian/Homo_sapiens/all_assembly_versions/GCF_000001405.25_GRCh37.p13/GCF_000001405.25_GRCh37.p13_assembly_structure/Primary_Assembly/assembled_chromosomes/FASTA/chrY.fna.gz>
##INFO=<ID=GENE,Number=.,Type=String,Description="Genes for this variant">
##INFO=<ID=HGVSG,Number=1,Type=String,Description="HGVS genomic notation for this variant">
##INFO=<ID=MMCNT1,Number=1,Type=Integer,Description="Count of Mastermind articles with cDNA matches for this specific variant">
##INFO=<ID=MMCNT2,Number=1,Type=Integer,Description="Count of Mastermind articles with variants either explicitly matching at the cDNA level or given only at protein level">
##INFO=<ID=MMCNT3,Number=1,Type=Integer,Description="Count of Mastermind articles including other DNA-level variants resulting in the same amino acid change">
##INFO=<ID=MMID3,Number=.,Type=String,Description="Mastermind variant identifiers, as gene:key, for MMCNT3">
##INFO=<ID=MMURI3,Number=.,Type=String,Description="Mastermind search URI for articles including other DNA-level variants resulting in the same amino acid change">
##createdDate=Fri, 14 Jun 2019 00:35:11 UTC
##fileTimestamp=2019-06-14T00:35:11Z
##reference=GRCh37.p13
##bcftools_normVersion=1.9+htslib-1.9
##bcftools_normCommand=norm -f /data/GCF_000001405.25_GRCh37.p13_genomic.fna.gz -c w -o /cvr/cvr_20190613.norm.vcf.gz -O z --threads 4 /cvr/cvr_20190613.raw.vcf.gz; Date=Fri Jun 14 00:35:40 2019
#CHROM POS ID REF ALT QUAL FILTER INFO
chr1 69090 . T TA . PASS HGVSG=chr1:g.69091dup;GENE=OR4F5;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=OR4F5:M1dup;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=OR4F5&mutation=OR4F5:M1dup&ref=cvr
chr1 861334 . A G . PASS HGVSG=chr1:g.861334A>G;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:I5V;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:I5V&ref=cvr
chr1 861334 . ATC GTA . PASS HGVSG=chr1:g.861334_861336delinsGTA;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:I5V;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:I5V&ref=cvr
chr1 861334 . ATC GTG . PASS HGVSG=chr1:g.861334_861336delinsGTG;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:I5V;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:I5V&ref=cvr
chr1 861334 . ATC GTT . PASS HGVSG=chr1:g.861334_861336delinsGTT;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:I5V;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:I5V&ref=cvr
chr1 865584 . G A . PASS HGVSG=chr1:g.865584G>A;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:R41Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:R41Q&ref=cvr
chr1 865584 . GG AA . PASS HGVSG=chr1:g.865584_865585delinsAA;GENE=SAMD11;MMCNT1=0;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:R41Q;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:R41Q&ref=cvr
chr1 865595 . A G . PASS HGVSG=chr1:g.865595A>G;GENE=SAMD11;MMCNT1=1;MMCNT2=1;MMCNT3=1;MMID3=SAMD11:K45E;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:K45E&ref=cvr
chr1 865595 . AAG GAA . PASS HGVSG=chr1:g.865595_865597delinsGAA;GENE=SAMD11;MMCNT1=0;MMCNT2=0;MMCNT3=1;MMID3=SAMD11:K45E;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:K45E&ref=cvr
chr1 871192 . C T . PASS HGVSG=chr1:g.871192C>T;GENE=SAMD11;MMCNT1=0;MMCNT2=0;MMCNT3=1;MMID3=SAMD11:R116C;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20diseases&gene=SAMD11&mutation=SAMD11:R116C&ref=cvr
chr1 871192 . CGC TGT . PASS HGVSG=chr1:g.871192_871194delinsTGT;GENE=SAMD11;MMCNT1=0;MMCNT2=0;MMCNT3=1;MMID3=SAMD11:R116C;MMURI3=https://mastermind.genomenon.com/detail?disease=all%20



bahsetmiş olduğum karşılık gelme durumu bu tabloya göre düzenleniyor.

[mhmtkrktr]

Senin ilk mesajdan bu şekilde istediğin sonucunu çıkarabilseydim, kendimi mesih falan ilan ederdim ben

Kod Seç Genişlet

sed -i  's/NC_000001.10/chr1/gi' /nerede/bu/dosya

Senin komutun eksiği "^" ile satırda karşılık gelen ilk terimin değişeceğini belirtmemen ve "/g" ile satırın devamında da uyumlu olan terimleri değiştir demen. Fakat noktadan sonra gelen sayı da standart değil.

Aşağıda ihtiyacına göre olanı deneyebilirsin.

Kod Seç Genişlet

NC_000001.(blabla) chr1
NC_000001.(blabla) chr1
NC_000002.(blabla) chr2
....
NC_000023.(blabla) chrX
NC_000024.(blabla) chrY[/quote]
[code]nc_to_chr(){ for s in `seq -w 1 24`;do k=${s#0*} ; ((k==23)) && k=X; ((k==24)) && k=Y; sed -i "s%^NC_0000${s}.[0-9]*%chr${k}%" "$1";echo -ne "\rConverted -- chr${k}";done;echo -e "\nCompleted -- `basename $1`";};nc_to_chr 'VCF_DOSYASI.vcf'

NC_000001.(blabla) chr1
NC_000001.(blabla) chr1
NC_000002.(blabla) chr2
...
NC_000023.(blabla) chr23
NC_000024.(blabla) chr24[/code]

Kod Seç Genişlet

nc_to_chr(){ for s in `seq -w 1 24`;do k=${s#0*}; sed -i "s%^NC_0000${s}.[0-9]*%chr${k}%" "$1";echo -ne "\rConverted -- chr${k}";done;echo -e "\nCompleted -- `basename $1`";};nc_to_chr 'VCF_DOSYASI.vcf'

Sonucu incelemek için dosyayı bölebilirsin. 50 parçaya bölünce metin editörleri kolayca açabiliyor.
https://forum.ubuntu-tr.net/index.php?topic=58402.msg636240#msg636240
Dosyanın orijinalini bozmadan $HOME/split dizinine çıkaracaktır.

[shigej38]

Sevgili [mention=648062]@mhmtkrktr[/mention]:

İlgin için teşekkür ederim.

Kod Seç Genişlet

nc_to_chr(){ for s in `seq -w 1 24`;do k=${s#0*} ; ((k==23)) && k=X; ((k==24)) && k=Y; sed -i "s%^NC_0000${s}.[0-9]*%chr${k}%" "$1";echo -ne "\rConverted -- chr${k}";done;echo -e "\nCompleted -- `basename $1`";};nc_to_chr 'VCF_DOSYASI.vcf'

bu komut ile işlemi halledebildim.

[Empat]

[mention=648081]@shigej38[/mention]
Sorununuz çözüldüyse, forum düzeninin sürdürülebilirliğine katkı sağlamak için, konu başlığınızı [Çözüldü] olarak işaretlemenizi rica ediyoruz.

Başka bir sorunun yanıtını bulamazsanız ya da bir sorunla karşılaşırsanız, yeni bir konu açabilirsiniz.

İyi forumlar.