User: Ana

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Ana10
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Posts by Ana

<prev • 25 results • page 1 of 3 • next >
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Comment: C: running a perl script multiple times; input and output files are required
... Thanks Pierre, I have some questions though find snp_table_files , so you mean I should give the path to my genotype files ? and what about output files? the script requires output files as well ...
written 1 day ago by Ana10
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Comment: C: running a perl script multiple times; input and output files are required
... parallel or sequentially does not really matter, I want to run this script for 500 files. I do not get any error message by runnign this code but nothing happens. I find my output directory empty.. Do you have any idea how can do this job? ...
written 1 day ago by Ana10
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running a perl script multiple times; input and output files are required
... Hi everyone, I want to run a perl script for multiple input files. I have searched a lot, but could not find any relevant solution for that. The script requires 2 input files and 1 output file; here is the first few lines #!/usr/bin/perl use warnings; use strict; unless (@ARGV == 3) ...
perl parallelization written 1 day ago by Ana10 • updated 1 day ago by Pierre Lindenbaum96k
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Comment: C: extract groups of SnPs and store them in separate files
... Thank Pierre for giving me the hint. I had forgotten "split". Actually it was quite easy. I simply used $ split -n 5000 geno.file ...
written 2 days ago by Ana10
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extract groups of SnPs and store them in separate files
... Hi all, I have a genotype file containing 500K SNPs (i.e 500000 lines), I want to create groups of SNPs taken every 5K and store each group in seperate files. This means take SNPs 1-5000 and store in file 1(I want to keep the whole line), take SNPs 5001-10000 and store in file 2, take SNPs 10001- 1 ...
snp subsetting written 2 days ago by Ana10
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Comment: C: how can I keep only those SNP in file "a" which match to SNPs in file "b"?
... Yes, grep can easily do the job for me. I did not try Python scripts though .... thanks guys ...
written 7 days ago by Ana10
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how can I keep only those SNP in file "a" which match to SNPs in file "b"?
... I have a file that I have filtered my SNPs for LD (in the example below;my.filtered.snp.id). I want to keep only these SNPs in my genotype matrix (geno_snp), I figured how to do it in R but the file is so big (~7GB) can not load it in R. I want to keep those lines (the whole line including snp.id an ...
row genotype file written 10 days ago by Ana10 • updated 9 days ago by WouterDeCoster20k
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Comment: C: filter 0,1,2 genotype matrix for LD
... oh no, I meant is there any other way that I could filter my genotype matrix for ld ? ...
written 13 days ago by Ana10
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(Closed) converting rows into columns and vice versa
... I have a table file (including 11 million SNPs) and simply I want to convert rows into columns and column into rows. something like this, this is my unput 7 2 2 0 6 0 2 0 0 0 2 2 0 0 2 this is my desired output 7 0 2 2 2 2 2 0 0 0 0 0 6 0 2 normall ...
table python rows colums written 5 weeks ago by Ana10 • updated 5 weeks ago by EagleEye4.2k
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Comment: C: restructure rows and columns in perl or python (Interleaving columns by row pair
... Thanks so much WouterDeCoster, it produced exactly the file I wished in less than 1 minute. ...
written 7 weeks ago by Ana10

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