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yechengxi / DBG2OLC

A genome assembler that reduces the computational time of human genome assembly from 400,000 CPU hours to 2,000 CPU hours, utilizing long erroneous 3GS sequencing reads and short accurate NGS sequencing reads.
GNU General Public License v3.0
66 stars 27 forks source link

no more ulimit necessary #41

Closed swarris closed 6 years ago

swarris commented 6 years ago

The file DBG2OLC/utility/split_reads_by_backbone.py can be changed to this (line 118 and further):

                new_fp = open(options.output_dir + '/' + str(id) + '.reads.fasta', 'a')
                new_fp.write('>' + tuple[0] + '\n' + tuple[1] + '\n')
                new_fp.close()

This will open and close the file each time it is needed. Might create additional IO overhead, but ulimit can be left intact. Very handy when you're not root.

javibio-git commented 6 years ago

Hello swarris,

This maybe a silly question:

Specifically, which part of the script needs to be changed? after the if or after the else statements?

Thanks!

swarris commented 6 years ago

I created a pull request with the changes.